Nice choice of the E minor Sinfonia: I think it's one of the more interesting of the minor-key sinfonie, for some reason. It has an odd wheedling, almost Eastern European quality to it that I find unusual. When I was much younger, I was all about the F minor and the D minor, but I rarely have the patience to play them now — late at night, maybe if I've been drinking and am feeling sentimental. They're powerful, intricate pieces, but sometimes a little more than I want to play.
Not that you asked, but my personal favorites are the C, Cm, D, E, Em, G, A, Am. I like the F major, but I haven't played it in a while and I have to be more careful reading it than I'd like. Those are the ones that I keep playing, just for fun. And, no, I can never keep the arpeggios straight in the B minor — in theory it can be done, certainly, but since nobody's paying me to do it, I just don't bother. Among the 2-Part Inventions, the C, Cm, Dm, A, and the Bb are really the only ones I come back to, sort of just for fun. It's pretty fun to play the C or the Dm as fast as possible, almost as a joke to myself. Although Gould clearly won that game with his amusing, blistering take on the Am.
Oh, I remember the reason I was thinking the WTCII Cm Prelude had some relationship to the Cm Partita's first movement: just the LH part in staggered octaves or other intervals. I think you could just sight-read it without much problem. The fugue is great, but it has some tricky syncopations: probably a little harder than the fugue from book I, but not by much.